Using Eclipse Juno Service Release 2 and Egit 3.00.201204220635. We have a repository that contains a sub-module (used as a lib, we do not edit the sub module in this repository) and very often we end up with merge FAILED due to the sub-module being DIRTY-IN-WORKTREE. But opening git bash and doing git merge works without a problem. The sub module is not dirty when using in git bash.

Is the a known problem? Are there any workarounds for it?

Very often it looks like the sub module is dirty even though you have not changed it? Is this also a known problem?

A side not are there any plans in implementing automatic update of sub module when switching branch because its pretty annoying to have to update the sub module every time you switch branch?